Immunology Flashcards
What is the basic sequence of events that occur during a viral infection?
There is a rise in type 1 interferon and a rise in NK cells that flattens out the viral replication. The adaptive immune response then begins – there is a rise in Cytotoxic T lymphocytes and antibodies, which allows the complete removal of virus from the body.
State some differences between innate and adaptive immune responses.
The innate immune response is present from birth. It is not very specific and it is fast acting. Innate immunity relies on pre-formed and rapidly synthesised components. Adaptive immune response is the opposite.
State the two types of triggers of the innate immune response and give an example of each.
DAMP – high extracellular ATP
PAMP – bacterial cell wall components
What does the acute phase response respond to?
It is an inflammatory response to tissue damage.
What is a main clinical feature of the acute phase response and what causes it?
Fever – caused by Interleukin-1
What are the acute phase proteins and what do they do?
C-reactive protein – this and serum amyloid protein bind to bacterial cell wall components
Serum amyloid protein
Mannan-binding lectin – binds to mannose, which isn’t commonly found in mammalian cells
These are soluble PRRs which, once bound, helps activate the complement system
What are the five classes of immunoglobulin and what are their distinct features?
G – monomer - 75% of serum Ig. It passes from mother to foetus. Involved in the secondary immune response.
A – dimer – found on mucosal surfaces – has a secretory component to resist degradation by proteases found in the mucosa
M – pentamer – has 10 binding sites so is good at agglutinating pathogens. Involved in the primary immune response.
E – monomer – binds to basophils and mast cells and aids degranulation – involved in immune responses
D – monomer – very low serum concentration – involved in B lymphocyte signalling
How do antibodies kill viruses?
Opsonisation – make them more easily phagocytosed
Binding and preventing entry
Activating complement
Antibody-Dependent Cell-Mediated Cytotoxicity (ADCC) – coating in antibody means that infected cells are more easily killed by NK cells
What is the difference between B cell receptors and T cell receptors?
B cell receptors are membrane-anchored forms of the antibody that the B cell will secrete if activated. It can bind to intact antigens.
T cell receptors can only bind to processed antigens, which are presented on MHC molecules.
Describe the process of clonal selection.
Lymphocytes circulate through the lymph until they meet its complementary antigen. When the lymphocyte meets its antigen it will bind and become activated and begin to replicate itself. This is called clonal expansion.
What are the three main types of antigen presenting cell and what do they do?
Macrophages, Dendritic Cells, B cells – they pick up antigens and move to the lymph nodes where circulating lymph nodes can find the antigens.
What are the primary lymphoid organs?
Bone marrow and thymus
What are the secondary lymphoid organs?
Lymph nodes, Spleen, Mucosa-Associated Lymphoid Tissue (MALT)
What is the general structure of the thymus gland?
Bi-lobed. Lobes are divided into lobules by septa. You get darker staining at the peripheries. You find hassall’s corpuscles that give rise to regulatory T lymphocytes.
How does the thymus change during infection?
It doesn’t
How does the thymus change with age?
The thymus gets smaller with age and thymic output decreases. More fatty tissue in the thymus.
How does the T cell repertoire in your body change as you grow older?
The number of T cells stays the same but the variety decreases. It becomes oligoclonal. There are more memory cells.
What are the names of lymphatic vessels that bring lymph to and from the lymph nodes?
Afferent – in; efferent - out
What are germinal centers and what do they indicate?
Germinal centers are accumulations of B cells – the germinal centers indicate the presence of on-going infection
Where do lymphocytes exit the circulation and enter tissues?
High endothelial venules
What is the immunological role of the spleen?
It filters the blood for antigens
Describe the organisation of lymphoid tissue around the arteries in the spleen.
White pulp (lymphocyte area) is right next to arteries. PALS (periarterial lymphatic sheath) is directly around the arteries and the B cell zone is beyond that. Germinal centers can form in the spleen as well.
What is a Peyer’s patch and what does it do?
Peyer’s patches are aggregates of lymphocytes found just below the intestinal epithelium. M cells in the epithelial layer sample antigens from the gut and deliver it to lymphocytes in the Peyer’s patch.
Which immune cells are found in the subcutaneous immune system?
Dendritic cells – Langerhans cells
Keratinocytes
Tissue resident macrophages
T Lymphocytes
What are the three receptor interactions involved in the extravasation of lymphocytes?
Selectin binding – weak interaction
Chemokine receptor binds to chemokine on the endothelial surface
Integrins on the lymphocytes bind to ICAM-1
Describe the sequence of events that occur when lymphocytes move out of the circulation.
The lymphocytes are initially rolling along the endothelial layer – selectins bind and slow down the rolling
Then the chemokine receptor on the lymphocyte will bind to the chemokine on the endothelial layer.
When the chemokine binds, the integrin will be changed to the high affinity state allowing it to bind with ICAM-1
What receptors do all T cells have?
CD3
What other types of receptor do T cells have?
90% of T cells have alpha-beta receptors and 10% have gamma-delta
Of the alpha-beta receptors: 2/3 have CD4 and 1/3 have CD8
What are the two main receptors that all B cells have?
CD19 and CD20
What is the role of follicular dendritic cells?
Presents antigens to B cells
What are the three main ways in which the innate immune system can detect pathogens?
PAMPs, DAMPs and missing self
What are the main phagocytic cells? List some important features.
Neurophils – 70% of circulating WBCs – granulocytes – multilobed nucleus
Monocytes/Macrophages – signal infection by releasing cytokines
Describe how neutrophils move out of the blood vessels and into tissue.
Similar to lymphocyte extravasation.
Initial binding is weak between selectins and selectin ligands – slows down the neutrophils
Due to infection, activated macrophages release chemokines that bind to the surface of endothelial cells.
The chemokine receptor on the neutrophils binds to the chemokines and promotes the integrin to the high affinity state.
The integrin then binds with the integrin ligand which immobilises the neutrophils.
Then the neutrophils can move into the tissue.
What are the two main opsonins for neutrophils?
Antibodies and complement
Describe the action of the two main opsonins.
Antibodies bind to antigens on the cell surface of pathogens.
Complement glycoproteins bind directly to the surface of the pathogen.
These act as adaptors and can then bind to the neutrophil, activating it and stimulating phagocytosis.
What are the mechanisms by which neutrophils kill phagocytosed pathogens?
Oxygen-dependent and oxygen-independent mechanisms.
What are cytokines? List some characteristics.
Cytokine are small secreted proteins that act as messengers. They are short-lived.
Give some examples of cytokines.
Interferons, Interleukins, Growth factors, chemokines, TNF
What are the three ways in which cytokines can act?
Paracrine, Endocrine, Autocrine
Describe the onset and consequences of septic shock.
Infection causes a massive release of alarm cytokines by activated macrophages (TNF-alpha and IL-1)
Low blood pressure + Increase in vascular permeability
What is the ‘Complement’ system?
It’s a system of soluble glycoproteins that complement the action of antibodies.
What are the three ways in which complement is activated? Explain how exactly they activate compliment.
Classical Pathway – antigen binding to antibody causes a conformational change – activates complement
Alternative Pathway – direct contact with the pathogen surface activates complement
Lectin pathway – activated by lectin (which is a PRR) binding to carbohydrates that are only found on pathogens
What happens to the cleaved fragments during the complement cascade?
They are pro-inflammatory molecules, which can bind to receptors on mast cells and cause degranulation giving rise to an inflammatory response.
Other than lysis and opsonisation, what are the two other roles of complement?
Activation of the inflammatory response (by binding to mast cells and macrophages) and clearance of immune complexes (antibody-antigen complexes must be removed before they cause inflammation of blood vessels)
What are the two types of mast cell?
Mucosal and Connective Tissue
What can activate mast cells?
Pro-inflammatory products from complement - ANAPHYLATOXINS
Describe, in full, a typical inflammatory response to a bacterial pathogen.
Bacterial infection will firstly activate tissue resident macrophages, which begin producing alarm cytokines and chemokines.
These cytokines recruit neutrophils and lymphocytes to the area of infection.
Complement is activated by the classical or alternative pathways.
The pro-inflammatory products of complement bind to mast cells and cause degranulation leading to an inflammatory response.
What acute phase proteins are involved in the systemic acute phase response?
C-reactive protein, mannan-binding lectin, fibrinogen and complement
State some basic features of NK cells.
They are large cytotoxic lymphocytes
They are granular
Secrete interferon gamma
Describe how NK cells communicate with target cells.
They don’t have antigen specific receptors.
Instead they have activating and inhibitory receptors and depending on the balance between the two signals they decide whether to attack the cell.
What are the two types of target cell recognition by NK cells? Explain how they work.
Missing Self – when infected, cells will downregulate the expression of MHC Class I, which acts as an inhibitory signal. The loss of the inhibitory signal means that NK cells are more likely to kill the target cells.
Induced Self – cells will change the pattern of their self-proteins due to stress. These stress-induced patterns will be recognised by activating receptors on NK cells and lysed.
What are the three secondary effector functions of antibodies once bound to antigens?
Opsonisation
Complement activation
Cell activation (e.g. mast cells)
Which immunoglobulin category do antibodies fall into
Gamma immunoglobulins
What type of bond holds together the chains in the immunoglobulin?
Disulphide bonds
What is an immunoglobulin domain?
Internal intrachain disulphide bond
What did scientists find when sequencing the amino acid sequence of the variable region on antibodies?
There are three hypervariable regions called the complementarity determining regions
What part of the variable region of the antibody binds to the antigen?
The complementarity determining regions are found at the end of the variable regions and interact with antigens
What forces are involved in antibody-antigen binding?
THEY ARE ALL NON-COVALENT
Hydrogen bonding, ionic bonding, van der waals, hydrophobic interactions
Define affinity.
The strength of the total non-covalent interactions between a single antigen-binding site and a single epitope
What equation shows affinity mathematically?
K = [Ab-Ag]/[free Ab][free Ag]
Define avidity.
The overall strength of the multiple interactions between an antibody with multiple binding sites and a complex antigen with multiple epitopes
What is antibody cross-reactivity? Give an example.
Antibodies that are produced in response to one antigen can cross-react and bind to a different antigen with a similar structure. E.g. cow pox and small pox
What are isotypes and allotypes of antibodies?
Isotypes vary in the constant regions – everyone has isotypes
Allotypes – polymorphic variables – some people have them others don’t
How do the different classes of antibodies (GAMED) differ?
They vary in the constant region of their heavy chain
What are the two classes of light chain?
Kappa and lambda
Which immunoglobulin classes have subclasses and how many subclasses do they have?
IgG = 4 (in order of abundance – 1 is the most abundant) IgA = 2
How do the different subclasses vary?
They vary in the hinge region
Describe the formation of secretory IgA.
Dimeric IgA is produced by plasma cells
It binds to the Poly-Ig receptor on the basolateral surface of the epithelia
This binding stimulates endocytosis
Once inside the cell, the poly-Ig receptor is cleaved and the dimeric IgA is secreted with the secretory component
The secretory component is derived from the poly-Ig receptor
How can IgE activate cells?
It binds to the Fc (Fc-epsilon-RI) receptor on mast cells
When antigens bind to the IgE, which is attached to the mast cell, it stimulates degranulation
Which two Ig classes are mainly responsible for activating complement?
IgM and IgG
What is the difference between the types of epitopes recognised by B cells and T cells?
T cells = sequences
B cells = structure (tertiary)
Describe the structure of the B cell receptor and how it transmits signals into the cell.
The BCR is a membrane-anchored antibody
It is associated with two transmembrane domains called Ig-alpha and Ig-beta which have cytoplasmic tails that are long enough to transmit a signal to the inside of the cell
Antigen binding to the BCR causes a conformational change, which drives signaling via the Ig-alpha Ig-beta heterodimer
What is the process by which B cells and T cells generate the variety in their receptors/antibodies?
Immunoglobulin Gene Rearrangement
Describe the generation of variation in the light chainWhat enzyme is involved in the removal of unused segments of DNA?
There are 70 different V and J regions
The B cell begins with germline DNA and it cuts out various V and J regions at random leaving only a few
This means that there is a large number of different combinations of segments forming a large number of different antigen specificities
Different splicing patterns give rise to more variation
Describe the generation of variation in the heavy chain.
Gene rearrangement is the same – the only difference is that the heavy chain also has a D region and has several different constant regions (determines class)
What enzyme is involved in the removal of unused segments of DNA?
V(D)J Recombinase
What gene encodes this enzyme and what disease is caused by the deficiency of this gene/enzyme?
Rag gene - SCID
What determines the class of the immunoglobulin?
The constant region of the heavy chain
In what order does the gene rearrangement take place?
The heavy chain undergoes rearrangement before the light chain
What three things can happen to B cells once they’ve recognised their antigens?
Become Plasma cells
Become Memory cells
Somatic Hypermutation and Affinity Maturation
What is the general rule about B cell and T cell activation?
It needs co-stimulation to be activated – antigen alone is not enough
What are the two pathways by which B cell production is achieved?
T dependent and T independent
Describe the T independent pathway.
This is associated with long polysaccharides with a repeating subunit
The repeating unit can bind to several BCRs and drive cross-linking
There will also be PAMPs such as LPS that provide co-stimulation
Describe the T dependent pathway.
Dendritic cells and B cells take up the antigen at the same time
B cells process and present the antigen on MHC Class II
Dendritic cells also present the SAME antigen on MHC Class II to a T helper cell
The T helper cell becomes activated and undergoes clonal selection
The T helper cell then moves to the lymph nodes, comes into contact with the B cell and activates it
Describe the process of immunoglobulin class switching.
T helper cells (once bound to the B cell) can release various cytokines – depending on the cytokine released, the immunoglobulin class can be switched
What drives the improvement of the immune response between primary and secondary exposures?
Somatic Hypermutation and Affinity Maturation
Describe the process of somatic hypermutation.
Point mutations are induced in the VDJ regions by (Activation-induced deaminase – AID) which cause slight conformational changes in the antigen-binding site.
If the change is beneficial and improves the binding between antibody and antigen then it survives
Otherwise the B cells are killed by apoptosis
What is the general structure of a T Cell Receptor?
It consists of an alpha and beta chain
Both chains have a variable region and a constant region
What other receptor are TCRs associated with and how does it transmit signals?
CD3 is present on all T lymphocytes and they have a longer cytoplasmic tail than the TCR
Signals from the TCR are transmitted to the internal compartment of the cell via the CD3 receptors
The tails of CD3 have tyrosine residues
When antigen binds to the TCR, phosphorylation of tyrosine occurs in the tails, which leads to many chemical cascades.
What class of MHC do CD4+ T cells bind to?
MHC Class II
What class of MHC do CD8+ T cells bind to?
MHC Class I
Where are immature thymocytes found in the thymus?
In the cortex – mature thymocytes are found in the medulla
Describe, in full, T cell development in the thymus.
T cells initially have no TCR or CD4/CD8 receptors
The beta chain of the TCR assembles first followed by the alpha chain
If the TCR is functional, the T cell goes on to express both CD4 and CD8 receptors
Depending on which MHC class it binds to it eventually ends up being only CD4+ or CD8+
What do CD4 and CD8 bind to?
They bind to the side of the MHC molecule
In what order does gene rearrangement take place?
Beta chain is rearranged first (VDJ recombination) and then the alpha chain (VJ recombination)
What percentage of thymocytes survive selection?
5%
Describe, in full, the structure of MHC Class I.
MHC Class I consists of a heavy alpha chain which is polymorphic and a beta-2 microglobulin chain which is the same in everyone
Only the alpha chain has a transmembrane domain
How does the light polypeptide associate to the heavy polypeptide in MHC Class I?
Non-covalent bonding
What part of MHC Class I is transmembrane?
Alpha chain
Describe, in full, the structure of MHC Class II.
MHC Class II consists of two polypeptides of a similar size, an alpha and a beta chain
Both chains have a transmembrane domain
What part of MHC Class II is transmembrane?
Both the alpha and beta chains have transmembrane domains
What is the difference between the types of peptides presented by Class I and Class II?
Class I presents peptides that are smaller than the MHC molecule
Class II presents peptides that are longer than the MHC molecule so it often has bits protruding out of the MHC molecule
Describe how the structure of MHC allows it to bind to a broad variety of peptides.
It has a binding motif that consists of binding pockets where you get particular amino acids binding in those positions – this is a feature that is conserved in most peptides
What is the name for the Human MHC region in the genome?
Human Leukocyte Antigen
What are the types of MHC Class I genes?
A, B and C
What are the types of MHC Class II genes?
DP, DQ, DR
How many types of MHC molecule can one person produce?
12 – 6 class I and 6 class II
What is an MHC haplotype?
Group of MHC alleles linked together on a single chromosome
Describe the process of antigen presentation via MHC Class I.
MHC Class I present endogenous antigens
Viral proteins are processed by a proteasome and move through TAP protein into the ER
In the ER, the MHC Class I molecule assembles and a chaperone protein aids its folding
Once it has fully assembled, it can move to the cell surface via the golgi apparatus
Describe antigen presentation via MHC Class II.
Antigens are endocytosed and move into the endocytic pathway.
Newly formed MHC Class II molecules enter the ER using a signal sequence
In the ER, the MHC Class II associates with an invariant chain (blocks the binding site to make sure molecules that are meant to be loaded onto MHC Class I aren’t loaded onto class II.)
The invariant chain has a signal sequence that directs the MHC towards the endocytic pathway.
As it moves into the endocytic pathway, the invariant chain is digested leaving only a clip protein.
The final step is the replacing of the clip protein by the antigen.
Broadly speaking, how do Cytotoxic T Lymphocytes kill infected cells?
Inducing apoptosis
What are the two mechanisms by which CTLs kill cells?
Granzyme + perforin – perforin makes a pore in the cell membrane through which granzyme can enter and trigger apoptosis
Fas ligand on T cell binds to Fas receptor on infected cell
When Fas has been engaged – it releases CASPASES
Both pathways upregulate CASPASES which drives apoptosis
What are the four main effector functions of CD4+ T Lymphocytes?
Macrophage Activation
B cell Activation
Delayed Type Hypersensitivity
Regulation
What are the two phases involved in Delayed Type Hypersensitivity?
Sensitisation – initial exposure to the antigen
Effector – delayed response
What are the five T helper cell subsets?
Th1 – inflammatory responses
Th2 – boosts anti-multicellular organism responses
Th17 – important in control of bacteria
Follicular T helper cells – essential for generation of isotype-switched antibodies
Treg – regulation of T cell responses
What is the main difference between T cell memory and B cell memory?
T cell memory doesn’t undergo isotype switching or affinity maturation – it does not get better
What is hypercytokinemia and sepsis?
When there is too much immune response
Too much cytokines in the blood
Sepsis – bacteria has crossed the mucosa and entered the blood stream
What are the two general principles of regulating the immune response?
Responses against pathogens decline as the infection is eliminated – this is driven by apoptosis of lymphocytes
Immunological tolerance to persistent antigens
Define Immunological Tolerance.
Specific unresponsiveness to an antigen that is induced by exposure of lymphocytes to the antigen
What are the two types of tolerance?
Central tolerance – destroy self-reactive B and T cells before they enter the circulation
Peripheral tolerance – destroy self-reactive B and T cells that do reach the circulation
What gene allows thymic expression of all the body’s gene products?
AIRE – autoimmune regulator
What does this gene encode?
Specialised transcription factor – allows thymic expression of all the body’s gene products
What are the four main mechanisms of peripheral tolerance?
Anergy
Deletion
Ignorance
Regulation
Describe each of the four processes.
Anergy – the way in which the APC presents the antigen shuts down the T cell and makes it unresponsiveness (sort of like increasing the activation energy by denying it of costimulation)
Deletion – antigen-induced cell death (apoptosis of T cell)
Ignorance – in some immuneprivileged sites there aren’t any APCs for the T cells to bind with
Regulation – regulation of response by cytokines released by Treg
What cytokine is frequently involved in shutting down dendritic cells?
IL-10
What transcription factor do Tregs express that is key to its function?
FoxP3
What are the two types of Treg?
Natural Tregs (nTreg) – develop in the thymus Inducible Tregs (iTreg) – when exposed to APCs they turn from T helper function to Treg function
